Mercurial > repos > galaxyp > cardinal_spectra_plots
view test-data/Example_Processed.imzML @ 8:ebb7de263d49 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d008f6ea0f5c8435fb975a34cb99ea4d42c5ebd2"
author | galaxyp |
---|---|
date | Wed, 13 May 2020 14:31:42 -0400 |
parents | 9b6b86e771c2 |
children |
line wrap: on
line source
<?xml version="1.0" encoding="ISO-8859-1"?> <mzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" xmlns="http://psi.hupo.org/ms/mzml" version="1.1"> <cvList count="4"> <cv URI="http://ontologies.berkeleybop.org/pato.obo" fullName="Phenotype And Trait Ontology" id="PATO" version="releases/2017-07-10"/> <cv URI="http://ontologies.berkeleybop.org/uo.obo" fullName="Units of Measurement Ontology" id="UO" version="releases/2017-09-25"/> <cv URI="https://raw.githubusercontent.com/hupo-psi/psi-ms-cv/master/psi-ms.obo" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" id="MS" version="4.1.0"/> <cv URI="https://raw.githubusercontent.com/imzML/imzML/master/imagingMS.obo" fullName="Mass Spectrometry Imaging Ontology" id="IMS" version="1.1.0"/> </cvList> <fileDescription> <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/> <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9d501bdc53444916b7e97e795b02c856"/> <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7e8fdb93053915d3edb51b70aa0619ac209964df"/> <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/> </fileContent> <sourceFileList count="1"> <sourceFile id="sf1" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\" name="Example.raw"> <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format"/> <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format"/> <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/> </sourceFile> </sourceFileList> <contact> <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/> <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Institut für Anorganische und Analytische Chemie"/> <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/> <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/> </contact> </fileDescription> <referenceableParamGroupList count="4"> <referenceableParamGroup id="mzArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/> </referenceableParamGroup> <referenceableParamGroup id="intensityArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/> </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan"/> <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/> </referenceableParamGroup> <referenceableParamGroup id="spectrum1"> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/> <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/> <cvParam cvRef="MS" accession="MS:1000129" name="negative scan"/> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> <sample id="sample1" name="Sample1"> <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/> </sample> </sampleList> <softwareList count="2"> <software id="Xcalibur" version="2.2"> <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur"/> </software> <software id="TMC" version="1.1 beta"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/> </software> </softwareList> <scanSettingsList count="1"> <scanSettings id="scansettings1"> <cvParam cvRef="IMS" accession="IMS:1000401" name="top down"/> <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback"/> <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan"/> <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right"/> <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixels x" value="3"/> <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixels y" value="3"/> <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/> <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/> <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size (x)" value="100.0" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/> <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100.0" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/> </scanSettings> </scanSettingsList> <instrumentConfigurationList count="1"> <instrumentConfiguration id="LTQFTUltra0"> <cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra"/> <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/> <componentList count="3"> <source order="1"> <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization"/> <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet"/> <cvParam cvRef="MS" accession="MS:1000844" name="focus diameter x" value="10.0"/> <cvParam cvRef="MS" accession="MS:1000845" name="focus diameter y" value="10.0"/> <cvParam cvRef="MS" accession="MS:1000846" name="pulse energy" value="10.0"/> <cvParam cvRef="MS" accession="MS:1000847" name="pulse duration" value="10.0"/> <cvParam cvRef="MS" accession="MS:1000848" name="attenuation" value="50.0"/> <cvParam cvRef="MS" accession="MS:1000850" name="gas laser"/> <cvParam cvRef="MS" accession="MS:1000836" name="dried droplet MALDI matrix preparation"/> <cvParam cvRef="MS" accession="MS:1000835" name="matrix solution concentration" value="10.0"/> <cvParam cvRef="MS" accession="MS:1000834" name="matrix solution" value="DHB"/> </source> <analyzer order="2"> <cvParam cvRef="MS" accession="MS:1000264" name="ion trap"/> <cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> </analyzer> <detector order="3"> <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier"/> <cvParam cvRef="MS" accession="MS:1000120" name="transient recorder"/> </detector> </componentList> <softwareRef ref="Xcalibur"/> </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="2"> <dataProcessing id="XcaliburProcessing"> <processingMethod softwareRef="Xcalibur" order="1"> <cvParam cvRef="MS" accession="MS:1000594" name="low intensity data point removal"/> </processingMethod> </dataProcessing> <dataProcessing id="TMCConversion"> <processingMethod softwareRef="TMC" order="2"> <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML"/> </processingMethod> </dataProcessing> </dataProcessingList> <run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44"> <spectrumList count="9" defaultDataProcessingRef="XcaliburProcessing"> <spectrum id="Scan=1" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="0"> <referenceableParamGroupRef ref="spectrum1"/> <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="121.85039039868471"/> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/> <scan instrumentConfigurationRef="LTQFTUltra0"> <referenceableParamGroupRef ref="scan1"/> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Scan=2" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="1"> <referenceableParamGroupRef ref="spectrum1"/> <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="182.31835420101888"/> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/> <scan instrumentConfigurationRef="LTQFTUltra0"> <referenceableParamGroupRef ref="scan1"/> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Scan=3" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="2"> <referenceableParamGroupRef ref="spectrum1"/> <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="161.8091904482675"/> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/> <scan instrumentConfigurationRef="LTQFTUltra0"> <referenceableParamGroupRef ref="scan1"/> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Scan=4" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="3"> <referenceableParamGroupRef ref="spectrum1"/> <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="200.9633277092539"/> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/> <scan instrumentConfigurationRef="LTQFTUltra0"> <referenceableParamGroupRef ref="scan1"/> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Scan=5" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="4"> <referenceableParamGroupRef ref="spectrum1"/> <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="135.30584173158496"/> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/> <scan instrumentConfigurationRef="LTQFTUltra0"> <referenceableParamGroupRef ref="scan1"/> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Scan=6" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="5"> <referenceableParamGroupRef ref="spectrum1"/> <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="108.39597418421639"/> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/> <scan instrumentConfigurationRef="LTQFTUltra0"> <referenceableParamGroupRef ref="scan1"/> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="335976"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="369572"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Scan=7" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="6"> <referenceableParamGroupRef ref="spectrum1"/> <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="127.84664447846832"/> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/> <scan instrumentConfigurationRef="LTQFTUltra0"> <referenceableParamGroupRef ref="scan1"/> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="403168"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="436764"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Scan=8" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="7"> <referenceableParamGroupRef ref="spectrum1"/> <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="168.27018147522492"/> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/> <scan instrumentConfigurationRef="LTQFTUltra0"> <referenceableParamGroupRef ref="scan1"/> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> <spectrum id="Scan=9" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="8"> <referenceableParamGroupRef ref="spectrum1"/> <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="243.5395066031077"/> <scanList count="1"> <cvParam cvRef="MS" accession="MS:1000795" name="no combination"/> <scan instrumentConfigurationRef="LTQFTUltra0"> <referenceableParamGroupRef ref="scan1"/> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/> </scan> </scanList> <binaryDataArrayList count="2"> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="mzArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> <binaryDataArray encodedLength="0"> <referenceableParamGroupRef ref="intensityArray"/> <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/> <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/> <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/> <binary /> </binaryDataArray> </binaryDataArrayList> </spectrum> </spectrumList> </run> </mzML>